ld: warning: in gtkscintilla2/libgtkscintilla2.a, file was built for unsupported file format which is not the architecture being linked (x86_64)

Actually with Xcode 4.5.2 and Apple clang 4.1 the wording has changed to:

ld: warning: ignoring file gtkscintilla2/libgtkscintilla2.a, file was built for archive which is not the architecture being linked (x86_64): gtkscintilla2/libgtkscintilla2.a

The attached port is updated to the final version of 0.9.98 fetched from the developer's github. Parallel building is disabled for now to ensure consistent error messages. The universal variant is enabled but has not been tested; it's blocked by #37774.

Searching on this error message I found #29261 (about a different port) in which Joshua said "Apparently it's trying to put an archive inside another archive, and ranlib doesn't support that." That seems to be the case here as well: it's trying to put an archive (scintilla.a) inside another archive (libgtkscintilla2.a).